Houk also skippered the Detroit Tigers and the Boston Red Sox in a managerial career that spanned three decades.
Red Sox spokesman Dick Bresciani said Houk's grandson, Scott Slaboden, told the team Houk died at his home in Winter Haven, Fla. Slaboden, who lives in the Boston area, wrote in an e-mail to the team that Houk "died peacefully of natural causes after having a brief illness."
Before reaching the big leagues with the Yankees in 1947, Houk served in the Army in World War II and rose to the rank of major - a moniker that stuck even when he returned to baseball.
Houk spent parts of eight seasons as a backup catcher for New York, appearing in just 91 games. Former Yankees shortstop Tony Kubek, who played for Houk in the minors and majors with New York, said Houk learned a lot about handling a pitching staff from working with Hall of Famer catchers Yogi Berra and Bill Dickey in the bullpen.
"He had the Yankees' spirit, the Yankees' winning attitude," Kubek told The Associated Press in a phone interview. "He had all the qualities that make a special manager."
Houk managed 3,157 games and won 1,619 with a winning percentage of .514. He followed Casey Stengel as Yankees manager in 1961 and was George Steinbrenner's first manager for New York in 1973. He resigned after one year working for the Boss and moved on to Detroit.
Houk managed the Tigers from 1974-78. His final stint in the dugout came with Boston from 1981-84.
"People forget that before he was a manager, he was a war hero and he was a catcher for a lot of years," Tigers radio analyst Jim Price said. "He was a great guy, I knew him very well, and everyone that played for him loved him."
It's been a tough couple of weeks for the Yankees organization, which has lost three notable figures from its storied history in the last 10 days. Longtime public address announcer Bob Sheppard died on July 11 and iconic owner Steinbrenner passed away two days later.
Houk's best seasons as a manager were his first three in New York. He took over the Yankees in 1961 and behind Mickey Mantle and Roger Maris the team won 109 games and a World Series championship.
The Yankees repeated as champions in 1962 and won the AL pennant in 1963, but were swept by the Los Angeles Dodgers in the World Series.
Houk managed a handful of Hall of Famers in New York, but Kubek said he was an integral part of the team's success.
"Sometimes when you have good players, you can mess it up and he didn't do that," he said. "He didn't overmanage. He was probably, more than a strategist, a handler of men."
Houk moved into the front office after the series loss to the Dodgers, serving as Yankees general manager in 1964 and '65. He returned to managing the Yankees in 1966 and held the job until 1973, but he only had four more winning seasons and never finished better than second place.
The Lawrence, Kan., native had only one winning season with the Tigers, his last in 1978.
"Ralph was a great baseball man who handled his players well and they played hard for him," Tigers Hall of Famer Al Kaline said in a statement released by the team. "He was well respected and a fun guy to be around. I enjoyed playing for him during my last year."
Longtime Braves manager Bobby Cox played for Houk with the Yankees in 1968-69.
"Great guy. Great guy," Cox said Wednesday night after Atlanta lost to San Diego in 12 innings. "Sorry to hear that. I love Ralph. He was just outstanding."
Houk came out of retirement at the age of 61 to become Red Sox manager. He had three winning seasons before retiring for good in 1984, leaving behind the core of a team that would reach the World Series in 1986.
"He was a great players' manager, a real good guy and a tough son of a gun," Dodgers manager Joe Torre said. "I got to know him after his managing days, and he's a great credit to the Yankees, Red Sox and Tigers organizations."
But he'll most be remembered as a Yankee.
"He was just a wonderful guy, loyal to his players," Kubek said. "The Major was just a great person."
Houk is survived by his daughter, Donna Houk Slaboden, his son Robert Houk and four grandchildren and 10 great-grandchildren.